An Associate with FXFOWLE recently posted her experience in taking a LEED-CI v2.0 project and switching it over into a LEED-CI 2009 on Building Green's Live Blog.* This very balanced look highlights some of the changes that caused frustration, but also those that made the process easier (notably the use of the Licensed Professional Exemption... more on that later). The article doesn't cover anything, but it's definitely worth reading if you're considering a similar switch.
*Building Green is the parent company of LEEDuser.com, a sponsor of RealLifeLEED. I promise that this post has nothing to do with said sponsorship... it's really a good read!